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- PDB-5ix8: Crystal structure of sugar ABC transport system, substrate-bindin... -

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Basic information

Entry
Database: PDB / ID: 5ix8
TitleCrystal structure of sugar ABC transport system, substrate-binding protein from Bordetella parapertussis 12822
ComponentsPutative sugar ABC transport system, substrate-binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / Midwest Center for Structural Genomics / MCSG / ABC transporter / solute binding protein
Function / homology
Function and homology information


Periplasmic binding protein / Periplasmic binding protein domain / Response regulator / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sugar ABC transport system, substrate-binding protein
Similarity search - Component
Biological speciesBordetella parapertussis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsChang, C. / Cuff, M. / Joachimiak, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM 115586 United States
CitationJournal: To Be Published
Title: Crystal structure of sugar ABC transport system, substrate-binding protein from Bordetella parapertussis 12822
Authors: Chang, C. / Cuff, M. / Joachimiak, G. / Clancy, S. / Joachimiak, A.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Structure summary
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sugar ABC transport system, substrate-binding protein
B: Putative sugar ABC transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,86713
Polymers69,9462
Non-polymers92111
Water10,413578
1
A: Putative sugar ABC transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3856
Polymers34,9731
Non-polymers4125
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative sugar ABC transport system, substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4817
Polymers34,9731
Non-polymers5086
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.557, 78.719, 66.890
Angle α, β, γ (deg.)90.000, 104.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative sugar ABC transport system, substrate-binding protein


Mass: 34972.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253) (bacteria)
Strain: 12822 / ATCC BAA-587 / NCTC 13253 / Gene: BPP2773 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q7W6X1
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Ammonium sulfate, Tris-Cl, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979291 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2013
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979291 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 101987 / % possible obs: 99.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.039 / Rrim(I) all: 0.084 / Χ2: 0.756 / Net I/av σ(I): 16.953 / Net I/σ(I): 7.5 / Num. measured all: 453878
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.46-1.492.61.1849120.3750.8031.4380.7595.2
1.49-1.513.21.07950700.4290.6721.2790.7699.3
1.51-1.543.81.08550450.5720.611.250.75499.9
1.54-1.574.30.9951100.6320.521.1220.762100
1.57-1.614.50.86151350.7280.4380.970.816100
1.61-1.644.60.72851280.8030.3620.8160.80999.9
1.64-1.694.70.63850820.8170.3150.7140.819100
1.69-1.734.70.51450910.880.2530.5750.85499.9
1.73-1.784.70.39751550.9220.1950.4430.8399.9
1.78-1.844.80.30250930.9440.1480.3380.858100
1.84-1.914.80.2351300.9590.1130.2570.8599.8
1.91-1.984.80.16650960.9730.0820.1860.8599.7
1.98-2.074.80.12951010.9810.0640.1440.82399.5
2.07-2.184.80.09851000.9860.0490.110.78699.4
2.18-2.324.80.07851020.9880.0390.0870.71199.3
2.32-2.54.80.06451180.990.0320.0720.67999.3
2.5-2.754.70.05651000.990.0290.0640.67899.5
2.75-3.154.60.04451290.9930.0230.050.58499.3
3.15-3.964.50.03551700.9940.0190.040.46899.5
3.96-504.50.04151200.9930.0220.0460.64397.6

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→24.983 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.69
RfactorNum. reflection% reflection
Rfree0.1808 3815 4.9 %
Rwork0.1395 --
obs0.1415 77787 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.53 Å2 / Biso mean: 17.6962 Å2 / Biso min: 7.01 Å2
Refinement stepCycle: final / Resolution: 1.6→24.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4839 0 64 578 5481
Biso mean--22.33 29.41 -
Num. residues----639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125079
X-RAY DIFFRACTIONf_angle_d1.1486924
X-RAY DIFFRACTIONf_chiral_restr0.07782
X-RAY DIFFRACTIONf_plane_restr0.008906
X-RAY DIFFRACTIONf_dihedral_angle_d12.1283059
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.62030.26311320.17742487261990
1.6203-1.64160.24661310.15762633276496
1.6416-1.66410.20381360.15522694283098
1.6641-1.68780.23771600.14792727288799
1.6878-1.7130.20031380.141927622900100
1.713-1.73980.20391200.136627642884100
1.7398-1.76830.19231530.131327402893100
1.7683-1.79880.21621400.125327952935100
1.7988-1.83150.20791270.126527572884100
1.8315-1.86670.1911420.124727712913100
1.8667-1.90480.17861450.124127342879100
1.9048-1.94620.17541440.121127382882100
1.9462-1.99140.17681600.127327542914100
1.9914-2.04120.16351460.1212742288899
2.0412-2.09640.20141620.122827492911100
2.0964-2.1580.17031700.12392729289999
2.158-2.22760.1661360.12482730286699
2.2276-2.30720.1751290.12822762289199
2.3072-2.39950.19161440.13442770291499
2.3995-2.50860.18641240.14122757288199
2.5086-2.64080.1761360.141427512887100
2.6408-2.8060.1751380.14632766290499
2.806-3.02230.16781290.14462763289299
3.0223-3.32580.17891480.14812769291799
3.3258-3.80560.16261380.139527892927100
3.8056-4.78920.16141460.13412765291199
4.7892-24.98640.18561410.1762774291597

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